13 Silent Signs Your Microbiome Could Be in Trouble

That collection of bacteria in your gut could have more wide-reaching health effects than you realize. Here are the warning signs that it's not happy.

Sirirat/ShutterstockYou have bad health habits

Your microbiome reveals surprising things about you—and likewise, your habits can also reveal surprising things about your gut health. “The microbiome of your digestive system, or the gut microbiome, contains perhaps 5,000 to 10,000 different species of bacteria that provide essential services of nutrition and protection,” says biochemist Erika Angle, PhD, the CEO and co-founder of Ixcela, the internal fitness company. “The makeup of your gut microbiome is determined by your genes—however, it is the organ that can be most influenced by your actions, for example diet, exercise, and stress management.” One Canadian animal study found those that were less stressed had healthier microbiomes.

You have GI problems

One of the things your bowel movements can reveal about your health is how healthy (or not) your gut microbiome is. Bloating, gas, indigestion, heartburn, diarrhea, and constipation can be caused by your gut flora being off. “These types of digestive issues often indicate a microbial imbalance in the gut,” says Frank Lipman, MD, bestselling author and founder of Be Well and the Eleven Eleven Wellness Center in New York City. “I often remedy this with a combination of diet recommendations, targeted supplements, and lifestyle practices.” Probiotics can also help get you back on track, he says. Studies have shown heartburn meds called proton-pump inhibitors, such as Prilosec, can ironically make gut bacteria less healthy. Here’s what you need to know about probiotics.

You’ve been in a bad mood

If you feel out of it, irritable, or have other mental issues, your microbiome could be to blame, according to the American Psychological Association. “Most neurotransmitters are actually made in the gut, so brain function is often a result of the health of our gut,” Dr. Lipman says. “If there is an imbalance of beneficial and harmful bacteria, it can manifest as problems with mental clarity and memory, along with signs of depression and anxiety.” One study from the UK found people that were given prebiotics, which feeds good gut bacteria, had lower anxiety. Find out other medical reasons that might be the source of your brain fog.

You get infections down there

One of the best ways to prevent yeast infections is to up your probiotic intake. “These types of infections can often be a result of systemic yeast, or fungal overgrowth in the gut,” Dr. Lipman says. This is why you’re more likely to get the nasty infections when you take antibiotics, which kill the good bacteria that help keep yeast in check along with the bad. Too much sugar in your diet can also feed the fungus. “The infections are quite common in our society as we are overexposed to antibiotics, environmental toxins, a diet in refined carbs and sugar, stress, and lack of sleep—the standard American way!” Dr. Lipman says. Check out these other ways to prevent yeast infections.

You have major sugar cravings

Your gut bacteria has been found in studies to actually influence the foods you desire. “Changes in microbiome composition have been shown to send signals to the brain, both direct nervous signals and biochemical signals, resulting in cravings for certain foods,” Dr. Angle says. An unhealthy, sugar-loving microbiome might crave sugar in turn, suggests research from Switzerland. In a vicious circle, “sugar feeds bad bacteria and yeast in the body, and therefore, a diet high in sugar and refined carbs will often lead to an overgrowth of harmful bacteria and yeast, which will compromise gut function,” Dr. Lipman says. He advises limiting sugar in your diet and eating wholesome, nutrient-dense foods such as leafy greens and other veggies, healthy fats, and good quality animal protein.” Here are more surprising ways you can kick your sugar addiction.

You’ve gained weight

Not surprisingly, if you have sugar or other unhealthy cravings, you’ll be more likely to gain weight. But in addition, research has shown that certain bacteria in your gut might make you more predisposed to obesity to begin with. A study in mice even showed that altering gut bacteria made the mice more likely to lose or gain weight. What’s more, “in connection with obesity, low levels of a compound produced only in the gut have been linked to Type 2 diabetes as a risk factor,” Dr. Angle says.

You get sick a lot

A healthy gut microbiome could add years to your life, according to research. The opposite is also true—an unhealthy microbiome could mean you get sick more often. “Seventy percent of the immune system surrounds the gut,” Dr. Lipman says. “So if the microbiome is in an imbalanced state, it will affect and often compromise immune function.” To support your immune system, he advises a good quality probiotic, supplements such as vitamin D, a diet full of antioxidant rich foods, and getting good sleep. Those are just some of the habits of people who never get sick.

You have skin problems

Even the condition of our skin is influenced by our gut microbiome—a Russian study found that over half of acne sufferers in their study had impaired intestinal microflora. In addition, “skin problems such as psoriasis or rosacea have been shown to be related to changes in the relative activity and levels of three different bacterial species,” Dr. Angle says. “Progress in the possible treatment of these conditions has been made by suppressing bacterial overgrowth of one of the species involved.” Or, try these natural supplements that could clear up your acne for good.

You have chronic sinus issues

You have the clear signs you have a sinus infection, but is your gut to blame? A study from the University of California San Francisco found that chronic sinus infections were linked with a lack of bacterial diversity, as well as a lack of certain bacteria, in the sinus microbiome—but the gut microbiome likely influences it as well, according to the study author. “Clearly, the gastrointestinal tract is a prime target for, perhaps, altering immune responses at sites remote from that niche,” study author Susan Lynch told NPR. Watch out for these signs you need to pay more attention to your gut health.

You have an autoimmune disease

Because of your gut’s connections to the immune system, autoimmune disease, in which your body attacks itself, has also been linked to an unhealthy microbiome. “Research has indicated that abnormal levels and/or species of gut microbiota are also suspect in causing or contributing to some autoimmune diseases—studies have shown links to Type 1 diabetes, multiple sclerosis, and lupus,” Dr. Angle says. “A possible mechanism suggested for MS is that certain species of bacteria produce biochemicals that directly affect the T-cells in the immune system, perhaps triggering demyelination [loss of the insulation around the nerves].” Here’s why millennials need to worry about autoimmune disease.

You have joint pain

Among the secrets pain doctors won’t tell you: Your joint pain may be affected by the type of bacteria living in your gut. “Gut dysbiosis [imbalance] is implicated in the development of chronic inflammatory diseases” that cause joint pain, Dr. Angle says. “Different specific changes in the microbiome have been linked to rheumatoid arthritis and spondyloarthritis” as well as psoriatic arthritis. “It is not yet clear if these changes are present before the diseases manifest or as a result of the disease,” she says. “However, they make a good case for maintaining optimal gut function as a long-term preventative measure.”

You have a leaky gut

Doctors believe that this chronic inflammation occurs when bacteria penetrate the gut wall, leading to leaky gut syndrome. “Certain species of gut bacteria produce compounds that help maintain the junctions between the cells of the intestinal wall,” Dr. Angle says. “Intestinal permeability, sometimes referred to as ‘leaky gut,’ is a broad term reflecting the loss of some connectivity in the cells of the gut wall, letting through compounds and sometimes organisms that can cause problems in the rest of the body.” Although researchers are still unraveling the cause and effect, there appears to be a connection between leaky gut and other gut problems, including inflammatory bowel disease, which encompasses Crohn’s and ulcerative colitis. Read about the silent signs you have leaky gut syndrome.

You’re allergic to everything

Allergies are on the rise—and you’re likely at risk. One theory behind why so many more of us are prone to allergies and asthma is that our gut microbiomes have been altered in the past couple of generations, likely due to diet changes and antibiotic use, according to the University of Utah. And this increased likelihood of allergies and asthma starts from birth—research from the University of California San Francisco found that specific microbes in babies’ guts predicted a threefold risk in allergies by age 2 and asthma by age 4.